Detailed Program (2016)


Where: 2016 BioImage Computing Workshop

When: October 9th, 2016

Venue: Oudemanhuispoort of the University of Amsterdam


08:45-09:00 Welcome and Introduction


Oral Session 1

9:00-09:40 (Invited talk) Charless Fowlkes (UC Irvine) – Learning to detect, segment, and classify biological structures

09:40-10:20 (Invited talk) Pascal Fua (EPFL) – Comparing synaptic structure in the cortex of adult and old mice

10:20-10:40 (Contributed talk) Deep convolutional neural networks for human embryonic cell counting, Aisha S. Khan, Stephen Gould, and Mathieu Salzmann (The Australian National University)

Poster Session 1 (10:40-12:00)

  • Measuring process dynamics and nuclear migration for clones of neural progenitor cells, Edgar Cardenas De La Hoz, Mark R. Winter, Maria Apostolopoulou, Sally Temple, Andrew R. Cohen (Drexel University – Philadelphia, Neural Stem Cell Institute – Rensselaer)


  • Single-image insect pose estimation by graph based geometric models and random forests, Minmin Shen, Le Duan, and Oliver Deussen (University of Konstanz)


  • Feature augmented deep neural networks for segmentation of cells, Sajith K. Sadanandan, Petter Ranefall, and Carolina Wählby (Uppsala University, SciLifeLab)


  • Dendritic spine shape analysis: A clustering perspective, Muhammad Usman Ghani, Ertunç Erdil, Sümeyra Demir Kanık, Ali Özgür Argunşah, Anna Hobbiss, Inbal Israely, Devrim Ünay, Tolga Taşdizen, Müjdat Ҫetin (Sabancı University Istanbul, Champalimaud Centre for the Unknown – Lisbon, Izmir University of Economics, University of Utah)


12:00-13:30 Lunch Break


Oral Session 2

13:30-14:10 (Invited talk) Jens Rittscher (University Oxford) – Monitoring complex biological environments

14:10-14:50 (Invited talk) Jeroen van der Laak (Radboud University Medical Center) – Challenges of using computer vision for evaluating whole-slide pathology images

14:50-15:10 (Contributed talk) Poisson point processes for solving stochastic inverse problems in fluorescence microscopy, Ihor Smal and Erik Meijering (Erasmus MC, University Medical Center Rotterdam)

Poster Session 2 (15:10-16:30)

  • Cell counting by regression using convolutional neural network, Yao Xue, Nilanjan Ray, Judith Hugh, Gilbert Bigras (University of Alberta)


  • 3-D density kernel estimation for counting in microscopy image volumes using 3-D image filters and random decision trees, Dominic Waithe, Martin Hailstone, Mukesh Kumar Lalwani, Richard Parton, Lu Yang, Roger Patient, Christian Eggeling, and Ilan Davis (University of Oxford)


  • Histopathology image categorization with discriminative dimension reduction of Fisher vectors, Yang Song, Qing Li, Heng Huang, Dagan Feng, Mei Chen, Weidong Cai (University of Sydney, University of Texas at Arlington, State University of New-York at Albany, Carnegie Mellon University)


  • Automatic detection and segmentation of exosomes in transmission electron microscopy, Karel Štĕpka, Martin Maška, Jakub Jozef Pálenik, Vendula Pospíchalová, Anna Kotrbova, Ladislav Ilkovics, Dobromila Klemová, Aleš Hampl, Vítĕzslav Bryja, and Pavel Matula (Masaryk University)


Oral Session 3

16:30-17:10 (Invited talk) Thomas Walter (Institut Curie, Ecole des Mines Paris) – Bioimage Informatics for Phenomics Exploring morphological phenotypes and spatial organization by large-scale screening approaches

17:10-17:50 (Invited talk) Gonzalo de Polavieja (Instituto Cajal, Madrid) – Tracking animals in groups from video

17:50-18:00 Closing